A new hypothesis for type 1 diabetes risk: The at-risk allele at rs3842753 associates with increased beta cell INS mRNA in a meta-analysis of single cell RNA sequencing data

ABSTRACT Type 1 diabetes is characterized by the autoimmune destruction of insulin secreting β cells. Genetic variations upstream at the insulin (INS) locus contribute to ~10% of type 1 diabetes heritable risk. Multiple studies showed an association between rs3842753 C/C genotype and type 1 diabetes susceptibility, but the molecular mechanisms remain unclear. To date, no large-scale studies have looked at the effect of genetic variation at rs3842753 on INS mRNA at the single cell level. We aligned all human islet single cell RNA sequencing datasets available to us in 2020 to the reference genome GRCh38.98 and genotyped rs3842753, integrating 2315 β cells and 1223 β-like cells from 13 A/A protected donors, 23 A/C heterozygous donors, and 35 C/C at-risk donors, including adults without diabetes and with type 2 diabetes. INS expression mean and variance were significantly higher in single β cells from females compared with males. Comparing across β cells and β-like cells, we found that rs3842753 C containing cells (either homozygous or heterozygous) had the highest INS expression. We also found that β cells with the rs3842753 C allele had significantly higher ER stress marker gene expression compared to the A/A homozygous genotype. These findings support the emerging concept that inherited risk of type 1 diabetes may be associated with inborn, persistent elevated insulin production which may lead to β cell ER stress and fragility.